| Previous changeset 25:d84caa5a98ad (2020-02-11) Next changeset 27:5b60313a6ce7 (2021-05-12) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb" |
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modified:
trinity.xml |
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added:
test-data/reads.left.fq.gz test-data/reads.right.fq.gz |
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| diff -r d84caa5a98ad -r 26d5493b20b6 test-data/reads.left.fq.gz |
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| Binary file test-data/reads.left.fq.gz has changed |
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| diff -r d84caa5a98ad -r 26d5493b20b6 test-data/reads.right.fq.gz |
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| Binary file test-data/reads.right.fq.gz has changed |
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| diff -r d84caa5a98ad -r 26d5493b20b6 trinity.xml --- a/trinity.xml Tue Feb 11 12:22:17 2020 -0500 +++ b/trinity.xml Fri Mar 19 21:43:30 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@"> +<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@+galaxy1"> <description>de novo assembly of RNA-Seq data</description> <macros> <import>macros.xml</import> @@ -139,7 +139,7 @@ <option value="paired_collection">Paired-end collection</option> </param> <when value="single"> - <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/> + <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Single-end reads" help=""/> <conditional name="strand"> <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> <when value="false"> @@ -153,12 +153,12 @@ </conditional> </when> <when value="paired"> - <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger" multiple="true" label="Left/Forward strand reads" /> - <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger" multiple="true" label="Right/Reverse strand reads" /> + <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Left/Forward strand reads" /> + <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger,fastqsanger.gz" multiple="true" label="Right/Reverse strand reads" /> <expand macro="input_paired_strand_jaccard" /> </when> <when value="paired_collection"> - <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/> + <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger,fastqsanger.gz" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/> <expand macro="input_paired_strand_jaccard" /> </when> </conditional> @@ -170,7 +170,7 @@ <option value="unmerged_paired_collection">Paired-end</option> </param> <when value="unmerged_single_collection"> - <param name="input" argument="--single" type="data" format="fasta,fastqsanger" label="Single-end reads" help="Elements of collection will NOT be merged"/> + <param name="input" argument="--single" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Single-end reads" help="Elements of collection will NOT be merged"/> <conditional name="strand"> <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> <when value="false"> @@ -184,7 +184,7 @@ </conditional> </when> <when value="unmerged_paired_collection"> - <param name="pair_input" type="data_collection" collection_type="paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Pair dataset collection. The paired datasets will NOT be merged"/> + <param name="pair_input" type="data_collection" collection_type="paired" format="fasta,fastqsanger,fastqsanger.gz" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Pair dataset collection. The paired datasets will NOT be merged"/> <expand macro="input_paired_strand_jaccard" /> </when> </conditional> @@ -224,8 +224,23 @@ <param name="paired_or_single" value="unmerged_paired_collection"/> <param name="pair_input"> <collection type="paired"> - <element name="forward" value="reads.left.fq" ftype="fastqsanger" /> - <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/> + <element name="forward" value="reads.left.fq" ftype="fastqsanger" /> + <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/> + </collection> + </param> + <param name="is_strand_specific" value="true"/> + <param name="norm" value="true"/> + <param name="library_type" value="RF"/> + <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" /> + <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" /> + </test> + <test> + <param name="pool_mode" value="No" /> + <param name="paired_or_single" value="unmerged_paired_collection"/> + <param name="pair_input"> + <collection type="paired"> + <element name="forward" value="reads.left.fq.gz" ftype="fastqsanger" /> + <element name="reverse" value="reads.right.fq.gz" ftype="fastqsanger"/> </collection> </param> <param name="is_strand_specific" value="true"/> |